1
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Häußermann L, Singh A, Swart EC. Two paralogous PHD finger proteins participate in natural genome editing in Paramecium tetraurelia. J Cell Sci 2024; 137:jcs261979. [PMID: 39212120 PMCID: PMC11385659 DOI: 10.1242/jcs.261979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 06/28/2024] [Indexed: 09/04/2024] Open
Abstract
The unicellular eukaryote Paramecium tetraurelia contains functionally distinct nuclei: germline micronuclei (MICs) and a somatic macronucleus (MAC). During sex, the MIC genome is reorganized into a new MAC genome and the old MAC is lost. Almost 45,000 unique internal eliminated sequences (IESs) distributed throughout the genome require precise excision to guarantee a functional new MAC genome. Here, we characterize a pair of paralogous PHD finger proteins involved in DNA elimination. DevPF1, the early-expressed paralog, is present in only some of the gametic and post-zygotic nuclei during meiosis. Both DevPF1 and DevPF2 localize in the new developing MACs, where IES excision occurs. Upon DevPF2 knockdown (KD), long IESs are preferentially retained and late-expressed small RNAs decrease; no length preference for retained IESs was observed in DevPF1-KD and development-specific small RNAs were abolished. The expression of at least two genes from the new MAC with roles in genome reorganization seems to be influenced by DevPF1- and DevPF2-KD. Thus, both PHD fingers are crucial for new MAC genome development, with distinct functions, potentially via regulation of non-coding and coding transcription in the MICs and new MACs.
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Affiliation(s)
- Lilia Häußermann
- Max Planck Institute for Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Aditi Singh
- Max Planck Institute for Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Estienne C Swart
- Max Planck Institute for Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
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2
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Xi S, Nguyen T, Murray S, Lorenz P, Mellor J. Size fractionated NET-Seq reveals a conserved architecture of transcription units around yeast genes. Yeast 2024; 41:222-241. [PMID: 38433440 DOI: 10.1002/yea.3931] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 02/06/2024] [Accepted: 02/09/2024] [Indexed: 03/05/2024] Open
Abstract
Genomes from yeast to humans are subject to pervasive transcription. A single round of pervasive transcription is sufficient to alter local chromatin conformation, nucleosome dynamics and gene expression, but is hard to distinguish from background signals. Size fractionated native elongating transcript sequencing (sfNET-Seq) was developed to precisely map nascent transcripts independent of expression levels. RNAPII-associated nascent transcripts are fractionation into different size ranges before library construction. When anchored to the transcription start sites (TSS) of annotated genes, the combined pattern of the output metagenes gives the expected reference pattern. Bioinformatic pattern matching to the reference pattern identified 9542 transcription units in Saccharomyces cerevisiae, of which 47% are coding and 53% are noncoding. In total, 3113 (33%) are unannotated noncoding transcription units. Anchoring all transcription units to the TSS or polyadenylation site (PAS) of annotated genes reveals distinctive architectures of linked pairs of divergent transcripts approximately 200nt apart. The Reb1 transcription factor is enriched 30nt downstream of the PAS only when an upstream (TSS -60nt with respect to PAS) noncoding transcription unit co-occurs with a downstream (TSS +150nt) coding transcription unit and acts to limit levels of upstream antisense transcripts. The potential for extensive transcriptional interference is evident from low abundance unannotated transcription units with variable TSS (median -240nt) initiating within a 500nt window upstream of, and transcribing over, the promoters of protein-coding genes. This study confirms a highly interleaved yeast genome with different types of transcription units altering the chromatin landscape in distinctive ways, with the potential to exert extensive regulatory control.
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Affiliation(s)
- Shidong Xi
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Tania Nguyen
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Struan Murray
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Phil Lorenz
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Jane Mellor
- Department of Biochemistry, University of Oxford, Oxford, UK
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3
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Benedum J, Franke V, Appel LM, Walch L, Bruno M, Schneeweiss R, Gruber J, Oberndorfer H, Frank E, Strobl X, Polyansky A, Zagrovic B, Akalin A, Slade D. The SPOC proteins DIDO3 and PHF3 co-regulate gene expression and neuronal differentiation. Nat Commun 2023; 14:7912. [PMID: 38036524 PMCID: PMC10689479 DOI: 10.1038/s41467-023-43724-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 11/17/2023] [Indexed: 12/02/2023] Open
Abstract
Transcription is regulated by a multitude of activators and repressors, which bind to the RNA polymerase II (Pol II) machinery and modulate its progression. Death-inducer obliterator 3 (DIDO3) and PHD finger protein 3 (PHF3) are paralogue proteins that regulate transcription elongation by docking onto phosphorylated serine-2 in the C-terminal domain (CTD) of Pol II through their SPOC domains. Here, we show that DIDO3 and PHF3 form a complex that bridges the Pol II elongation machinery with chromatin and RNA processing factors and tethers Pol II in a phase-separated microenvironment. Their SPOC domains and C-terminal intrinsically disordered regions are critical for transcription regulation. PHF3 and DIDO exert cooperative and antagonistic effects on the expression of neuronal genes and are both essential for neuronal differentiation. In the absence of PHF3, DIDO3 is upregulated as a compensatory mechanism. In addition to shared gene targets, DIDO specifically regulates genes required for lipid metabolism. Collectively, our work reveals multiple layers of gene expression regulation by the DIDO3 and PHF3 paralogues, which have specific, co-regulatory and redundant functions in transcription.
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Affiliation(s)
- Johannes Benedum
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
- Department of Radiation Oncology, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Vedran Franke
- The Berlin Institute for Medical Systems Biology, Max Delbrück Center, Berlin, Germany
| | - Lisa-Marie Appel
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
- Department of Radiation Oncology, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Lena Walch
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
| | - Melania Bruno
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
| | - Rebecca Schneeweiss
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
| | - Juliane Gruber
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
| | - Helena Oberndorfer
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
| | - Emma Frank
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
| | - Xué Strobl
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Anton Polyansky
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Bojan Zagrovic
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Altuna Akalin
- The Berlin Institute for Medical Systems Biology, Max Delbrück Center, Berlin, Germany
| | - Dea Slade
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria.
- Department of Radiation Oncology, Medical University of Vienna, Vienna, Austria.
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria.
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4
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Carreras-Villaseñor N, Martínez-Rodríguez LA, Ibarra-Laclette E, Monribot-Villanueva JL, Rodríguez-Haas B, Guerrero-Analco JA, Sánchez-Rangel D. The biological relevance of the FspTF transcription factor, homologous of Bqt4, in Fusarium sp. associated with the ambrosia beetle Xylosandrus morigerus. Front Microbiol 2023; 14:1224096. [PMID: 37520351 PMCID: PMC10375492 DOI: 10.3389/fmicb.2023.1224096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 06/22/2023] [Indexed: 08/01/2023] Open
Abstract
Transcription factors in phytopathogenic fungi are key players due to their gene expression regulation leading to fungal growth and pathogenicity. The KilA-N family encompasses transcription factors unique to fungi, and the Bqt4 subfamily is included in it and is poorly understood in filamentous fungi. In this study, we evaluated the role in growth and pathogenesis of the homologous of Bqt4, FspTF, in Fusarium sp. isolated from the ambrosia beetle Xylosandrus morigerus through the characterization of a CRISPR/Cas9 edited strain in Fsptf. The phenotypic analysis revealed that TF65-6, the edited strain, modified its mycelia growth and conidia production, exhibited affectation in mycelia and culture pigmentation, and in the response to certain stress conditions. In addition, the plant infection process was compromised. Untargeted metabolomic and transcriptomic analysis, clearly showed that FspTF may regulate secondary metabolism, transmembrane transport, virulence, and diverse metabolic pathways such as lipid metabolism, and signal transduction. These data highlight for the first time the biological relevance of an orthologue of Bqt4 in Fusarium sp. associated with an ambrosia beetle.
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Affiliation(s)
- Nohemí Carreras-Villaseñor
- Laboratorios de Biología Molecular y Fitopatología, Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
| | - Luis A. Martínez-Rodríguez
- Laboratorios de Biología Molecular y Fitopatología, Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
| | - Enrique Ibarra-Laclette
- Laboratorio de Genómica y Transcriptómica, Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
| | - Juan L. Monribot-Villanueva
- Laboratorio de Química de Productos Naturales, Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
| | - Benjamín Rodríguez-Haas
- Laboratorios de Biología Molecular y Fitopatología, Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
| | - José A. Guerrero-Analco
- Laboratorio de Química de Productos Naturales, Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
| | - Diana Sánchez-Rangel
- Laboratorios de Biología Molecular y Fitopatología, Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
- Investigadora Por Mexico-CONAHCyT, Xalapa, Mexico
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5
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Wang B, Zhou X, Kettenbach AN, Mitchell HD, Markillie LM, Loros JJ, Dunlap JC. A crucial role for dynamic expression of components encoding the negative arm of the circadian clock. Nat Commun 2023; 14:3371. [PMID: 37291101 PMCID: PMC10250352 DOI: 10.1038/s41467-023-38817-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 05/17/2023] [Indexed: 06/10/2023] Open
Abstract
In the Neurospora circadian system, the White Collar Complex (WCC) drives expression of the principal circadian negative arm component frequency (frq). FRQ interacts with FRH (FRQ-interacting RNA helicase) and CKI, forming a stable complex that represses its own expression by inhibiting WCC. In this study, a genetic screen identified a gene, designated as brd-8, that encodes a conserved auxiliary subunit of the NuA4 histone acetylation complex. Loss of brd-8 reduces H4 acetylation and RNA polymerase (Pol) II occupancy at frq and other known circadian genes, and leads to a long circadian period, delayed phase, and defective overt circadian output at some temperatures. In addition to strongly associating with the NuA4 histone acetyltransferase complex, BRD-8 is also found complexed with the transcription elongation regulator BYE-1. Expression of brd-8, bye-1, histone h2a.z, and several NuA4 subunits is controlled by the circadian clock, indicating that the molecular clock both regulates the basic chromatin status and is regulated by changes in chromatin. Taken together, our data identify auxiliary elements of the fungal NuA4 complex having homology to mammalian components, which along with conventional NuA4 subunits, are required for timely and dynamic frq expression and thereby a normal and persistent circadian rhythm.
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Affiliation(s)
- Bin Wang
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA.
| | - Xiaoying Zhou
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
| | - Arminja N Kettenbach
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
| | - Hugh D Mitchell
- Biological Sciences Divisions, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Lye Meng Markillie
- Biological Sciences Divisions, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Jennifer J Loros
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
| | - Jay C Dunlap
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA.
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6
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Deshpande N, Bryk M. Diverse and dynamic forms of gene regulation by the S. cerevisiae histone methyltransferase Set1. Curr Genet 2023; 69:91-114. [PMID: 37000206 DOI: 10.1007/s00294-023-01265-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 03/11/2023] [Accepted: 03/14/2023] [Indexed: 04/01/2023]
Abstract
Gene transcription is an essential and highly regulated process. In eukaryotic cells, the structural organization of nucleosomes with DNA wrapped around histone proteins impedes transcription. Chromatin remodelers, transcription factors, co-activators, and histone-modifying enzymes work together to make DNA accessible to RNA polymerase. Histone lysine methylation can positively or negatively regulate gene transcription. Methylation of histone 3 lysine 4 by SET-domain-containing proteins is evolutionarily conserved from yeast to humans. In higher eukaryotes, mutations in SET-domain proteins are associated with defects in the development and segmentation of embryos, skeletal and muscle development, and diseases, including several leukemias. Since histone methyltransferases are evolutionarily conserved, the mechanisms of gene regulation mediated by these enzymes are also conserved. Budding yeast Saccharomyces cerevisiae is an excellent model system to study the impact of histone 3 lysine 4 (H3K4) methylation on eukaryotic gene regulation. Unlike larger eukaryotes, yeast cells have only one enzyme that catalyzes H3K4 methylation, Set1. In this review, we summarize current knowledge about the impact of Set1-catalyzed H3K4 methylation on gene transcription in S. cerevisiae. We describe the COMPASS complex, factors that influence H3K4 methylation, and the roles of Set1 in gene silencing at telomeres and heterochromatin, as well as repression and activation at euchromatic loci. We also discuss proteins that "read" H3K4 methyl marks to regulate transcription and summarize alternate functions for Set1 beyond H3K4 methylation.
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Affiliation(s)
- Neha Deshpande
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Mary Bryk
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.
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7
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Wang B, Zhou X, Kettenbach AN, Mitchell HD, Markillie LM, Loros JJ, Dunlap JC. A crucial role for dynamic expression of components encoding the negative arm of the circadian clock. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.24.538162. [PMID: 37162945 PMCID: PMC10168201 DOI: 10.1101/2023.04.24.538162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
In the Neurospora circadian system, the White Collar Complex (WCC) drives expression of the principal circadian negative arm component frequency ( frq ). FRQ interacts with FRH (FRQ-interacting helicase) and CK-1 forming a stable complex that represses its own expression by inhibiting WCC. In this study, a genetic screen identified a gene, designated as brd-8 , that encodes a conserved auxiliary subunit of the NuA4 histone acetylation complex. Loss of brd-8 reduces H4 acetylation and RNA polymerase (Pol) II occupancy at frq and other known circadian genes, and leads to a long circadian period, delayed phase, and defective overt circadian output at some temperatures. In addition to strongly associating with the NuA4 histone acetyltransferase complex, BRD-8 is also found complexed with the transcription elongation regulator BYE-1. Expression of brd-8, bye-1, histone hH2Az , and several NuA4 subunits is controlled by the circadian clock, indicating that the molecular clock both regulates the basic chromatin status and is regulated by changes in chromatin. Taken together, our data identify new auxiliary elements of the fungal NuA4 complex having homology to mammalian components, which along with conventional NuA4 subunits, are required for timely and dynamic frq expression and thereby a normal and persistent circadian rhythm.
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8
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Appel LM, Benedum J, Engl M, Platzer S, Schleiffer A, Strobl X, Slade D. SPOC domain proteins in health and disease. Genes Dev 2023; 37:140-170. [PMID: 36927757 PMCID: PMC10111866 DOI: 10.1101/gad.350314.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Since it was first described >20 yr ago, the SPOC domain (Spen paralog and ortholog C-terminal domain) has been identified in many proteins all across eukaryotic species. SPOC-containing proteins regulate gene expression on various levels ranging from transcription to RNA processing, modification, export, and stability, as well as X-chromosome inactivation. Their manifold roles in controlling transcriptional output implicate them in a plethora of developmental processes, and their misregulation is often associated with cancer. Here, we provide an overview of the biophysical properties of the SPOC domain and its interaction with phosphorylated binding partners, the phylogenetic origin of SPOC domain proteins, the diverse functions of mammalian SPOC proteins and their homologs, the mechanisms by which they regulate differentiation and development, and their roles in cancer.
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Affiliation(s)
- Lisa-Marie Appel
- Department of Radiation Oncology, Medical University of Vienna, 1090 Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
| | - Johannes Benedum
- Department of Radiation Oncology, Medical University of Vienna, 1090 Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Magdalena Engl
- Department of Radiation Oncology, Medical University of Vienna, 1090 Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Sebastian Platzer
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology (IMP), 1030 Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Xué Strobl
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Dea Slade
- Department of Radiation Oncology, Medical University of Vienna, 1090 Vienna, Austria;
- Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
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9
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Appel LM, Franke V, Benedum J, Grishkovskaya I, Strobl X, Polyansky A, Ammann G, Platzer S, Neudolt A, Wunder A, Walch L, Kaiser S, Zagrovic B, Djinovic-Carugo K, Akalin A, Slade D. The SPOC domain is a phosphoserine binding module that bridges transcription machinery with co- and post-transcriptional regulators. Nat Commun 2023; 14:166. [PMID: 36631525 PMCID: PMC9834408 DOI: 10.1038/s41467-023-35853-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 01/05/2023] [Indexed: 01/13/2023] Open
Abstract
The heptad repeats of the C-terminal domain (CTD) of RNA polymerase II (Pol II) are extensively modified throughout the transcription cycle. The CTD coordinates RNA synthesis and processing by recruiting transcription regulators as well as RNA capping, splicing and 3'end processing factors. The SPOC domain of PHF3 was recently identified as a CTD reader domain specifically binding to phosphorylated serine-2 residues in adjacent CTD repeats. Here, we establish the SPOC domains of the human proteins DIDO, SHARP (also known as SPEN) and RBM15 as phosphoserine binding modules that can act as CTD readers but also recognize other phosphorylated binding partners. We report the crystal structure of SHARP SPOC in complex with CTD and identify the molecular determinants for its specific binding to phosphorylated serine-5. PHF3 and DIDO SPOC domains preferentially interact with the Pol II elongation complex, while RBM15 and SHARP SPOC domains engage with writers and readers of m6A, the most abundant RNA modification. RBM15 positively regulates m6A levels and mRNA stability in a SPOC-dependent manner, while SHARP SPOC is essential for its localization to inactive X-chromosomes. Our findings suggest that the SPOC domain is a major interface between the transcription machinery and regulators of transcription and co-transcriptional processes.
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Affiliation(s)
- Lisa-Marie Appel
- Department of Radiation Oncology, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - Vedran Franke
- The Berlin Institute for Medical Systems Biology, Max Delbrück Center, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Johannes Benedum
- Department of Radiation Oncology, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Dr. Bohr-Gasse 9, 1030, Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, 1030, Vienna, Austria
| | - Irina Grishkovskaya
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Xué Strobl
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Dr. Bohr-Gasse 9, 1030, Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, 1030, Vienna, Austria
| | - Anton Polyansky
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Gregor Ammann
- Department of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt, Germany
| | - Sebastian Platzer
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - Andrea Neudolt
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - Anna Wunder
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - Lena Walch
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - Stefanie Kaiser
- Department of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt, Germany
| | - Bojan Zagrovic
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Kristina Djinovic-Carugo
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter, Campus Vienna Biocenter 5, 1030, Vienna, Austria
- Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecčna Pot 113, 1000, Ljubljana, Slovenia
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs, CS 90181, 38042, Grenoble, Cedex 9, France
| | - Altuna Akalin
- The Berlin Institute for Medical Systems Biology, Max Delbrück Center, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Dea Slade
- Department of Radiation Oncology, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria.
- Comprehensive Cancer Center, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria.
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Dr. Bohr-Gasse 9, 1030, Vienna, Austria.
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10
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Appel LM, Franke V, Bruno M, Grishkovskaya I, Kasiliauskaite A, Kaufmann T, Schoeberl UE, Puchinger MG, Kostrhon S, Ebenwaldner C, Sebesta M, Beltzung E, Mechtler K, Lin G, Vlasova A, Leeb M, Pavri R, Stark A, Akalin A, Stefl R, Bernecky C, Djinovic-Carugo K, Slade D. PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. Nat Commun 2021; 12:6078. [PMID: 34667177 PMCID: PMC8526623 DOI: 10.1038/s41467-021-26360-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 09/29/2021] [Indexed: 12/16/2022] Open
Abstract
The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) is a regulatory hub for transcription and RNA processing. Here, we identify PHD-finger protein 3 (PHF3) as a regulator of transcription and mRNA stability that docks onto Pol II CTD through its SPOC domain. We characterize SPOC as a CTD reader domain that preferentially binds two phosphorylated Serine-2 marks in adjacent CTD repeats. PHF3 drives liquid-liquid phase separation of phosphorylated Pol II, colocalizes with Pol II clusters and tracks with Pol II across the length of genes. PHF3 knock-out or SPOC deletion in human cells results in increased Pol II stalling, reduced elongation rate and an increase in mRNA stability, with marked derepression of neuronal genes. Key neuronal genes are aberrantly expressed in Phf3 knock-out mouse embryonic stem cells, resulting in impaired neuronal differentiation. Our data suggest that PHF3 acts as a prominent effector of neuronal gene regulation by bridging transcription with mRNA decay.
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Affiliation(s)
- Lisa-Marie Appel
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Vedran Franke
- The Berlin Institute for Medical Systems Biology, Max Delbrück Center, Berlin, Germany
| | - Melania Bruno
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Irina Grishkovskaya
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Aiste Kasiliauskaite
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Tanja Kaufmann
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Ursula E Schoeberl
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Martin G Puchinger
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Sebastian Kostrhon
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Carmen Ebenwaldner
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Marek Sebesta
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Etienne Beltzung
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, Vienna Biocenter (VBC), Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Gen Lin
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, Vienna Biocenter (VBC), Vienna, Austria
| | - Anna Vlasova
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, Vienna Biocenter (VBC), Vienna, Austria
| | - Martin Leeb
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Rushad Pavri
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, Vienna Biocenter (VBC), Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, Vienna Biocenter (VBC), Vienna, Austria
| | - Altuna Akalin
- The Berlin Institute for Medical Systems Biology, Max Delbrück Center, Berlin, Germany
| | - Richard Stefl
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Carrie Bernecky
- Institute of Science and Technology Austria (IST Austria), Am Campus 1, Klosterneuburg, Austria
| | - Kristina Djinovic-Carugo
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
- Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Dea Slade
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria.
- Department of Radiation Oncology, Medical University of Vienna, Vienna, Austria.
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria.
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11
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Jiang Z, Xiao SR, Liu R. Dissecting and predicting different types of binding sites in nucleic acids based on structural information. Brief Bioinform 2021; 23:6384399. [PMID: 34624074 PMCID: PMC8769709 DOI: 10.1093/bib/bbab411] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/26/2021] [Accepted: 09/07/2021] [Indexed: 12/16/2022] Open
Abstract
The biological functions of DNA and RNA generally depend on their interactions with other molecules, such as small ligands, proteins and nucleic acids. However, our knowledge of the nucleic acid binding sites for different interaction partners is very limited, and identification of these critical binding regions is not a trivial work. Herein, we performed a comprehensive comparison between binding and nonbinding sites and among different categories of binding sites in these two nucleic acid classes. From the structural perspective, RNA may interact with ligands through forming binding pockets and contact proteins and nucleic acids using protruding surfaces, while DNA may adopt regions closer to the middle of the chain to make contacts with other molecules. Based on structural information, we established a feature-based ensemble learning classifier to identify the binding sites by fully using the interplay among different machine learning algorithms, feature spaces and sample spaces. Meanwhile, we designed a template-based classifier by exploiting structural conservation. The complementarity between the two classifiers motivated us to build an integrative framework for improving prediction performance. Moreover, we utilized a post-processing procedure based on the random walk algorithm to further correct the integrative predictions. Our unified prediction framework yielded promising results for different binding sites and outperformed existing methods.
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Affiliation(s)
- Zheng Jiang
- College of Informatics, Huazhong Agricultural University, Wuhan, P. R. China
| | - Si-Rui Xiao
- College of Informatics, Huazhong Agricultural University, Wuhan, P. R. China
| | - Rong Liu
- College of Informatics, Huazhong Agricultural University, Wuhan, P. R. China
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12
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van Leeuwe TM, Arentshorst M, Punt PJ, Ram AF. Interrogation of the cell wall integrity pathway in Aspergillus niger identifies a putative negative regulator of transcription involved in chitin deposition. Gene 2021; 763S:100028. [PMID: 32550555 PMCID: PMC7285910 DOI: 10.1016/j.gene.2020.100028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/18/2019] [Accepted: 01/23/2020] [Indexed: 01/26/2023]
Abstract
Post-fermentation fungal biomass waste provides a viable source for chitin. Cell wall chitin of filamentous fungi, and in particular its de-N-acetylated derivative chitosan, has a wide range of commercial applications. Although the cell wall of filamentous fungi comprises 10–30% chitin, these yields are too low for cost-effective production. Therefore, we aimed to identify the genes involved in increased chitin deposition by screening a collection of UV-derived cell wall mutants in Aspergillus niger. This screen revealed a mutant strain (RD15.4#55) that showed a 30–40% increase in cell wall chitin compared to the wild type. In addition to the cell wall chitin phenotype, this strain also exhibited sensitivity to SDS and produces an unknown yellow pigment. Genome sequencing combined with classical genetic linkage analysis identified two mutated genes on chromosome VII that were linked with the mutant phenotype. Single gene knockouts and subsequent complementation analysis revealed that an 8 bp deletion in NRRL3_09595 is solely responsible for the associated phenotypes of RD15.4#55. The mutated gene, which was named cwcA (cell wall chitin A), encodes an orthologue of Saccharomyces cerevisiae Bypass of ESS1 (BYE1), a negative regulator of transcription elongation. We propose that this conserved fungal protein is involved in preventing cell wall integrity signaling under non-inducing conditions, where loss of function results in constitutive activation of the cell wall stress response pathway, and consequently leads to increased chitin content in the mutant cell wall. An Aspergillus niger UV-mutant with increased cell wall chitin was characterized. Causative mutation was identified in a single gene, named cell wall chitin A (cwcA). CwcA is orthologous to yeast Bye1p and exists as a single copy gene. Three relevant domains are found in both CwcA and Bye1p: PHD, TFIIS and SPOC. CwcA acts as negative regulator of CWI signaling.
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Affiliation(s)
- Tim M. van Leeuwe
- Leiden University, Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - Mark Arentshorst
- Leiden University, Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - Peter J. Punt
- Leiden University, Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Sylviusweg 72, 2333 BE Leiden, the Netherlands
- Dutch DNA Biotech, Hugo R Kruytgebouw 4-Noord, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Arthur F.J. Ram
- Leiden University, Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Sylviusweg 72, 2333 BE Leiden, the Netherlands
- Corresponding author at: Leiden University, Institute of Biology, Department Molecular Microbiology and Biotechnology, Sylviusweg 72, 2333 BE Leiden, the Netherlands.
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13
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Mora Gallardo C, Sánchez de Diego A, Martínez-A C, van Wely KHM. Interplay between splicing and transcriptional pausing exerts genome-wide control over alternative polyadenylation. Transcription 2021; 12:55-71. [PMID: 34365909 PMCID: PMC8555548 DOI: 10.1080/21541264.2021.1959244] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Recent studies have identified multiple polyadenylation sites in nearly all mammalian genes. Although these are interpreted as evidence for alternative polyadenylation, our knowledge of the underlying mechanisms is still limited. Most studies only consider the immediate surroundings of gene ends, even though in vitro experiments have uncovered the involvement of external factors such as splicing. Whereas in vivo splicing manipulation was impracticable until recently, we now used mutants in the Death Inducer Obliterator (DIDO) gene to study their impact on 3ʹ end processing. We observe multiple rounds of readthrough and gene fusions, suggesting that no arbitration between polyadenylation sites occurs. Instead, a window of opportunity seems to control end processing. Through the identification of T-rich sequence motifs, our data indicate that splicing and transcriptional pausing interact to regulate alternative polyadenylation. We propose that 3ʹ splice site activation comprises a variable timer, which determines how long transcription proceeds before polyadenylation signals are recognized. Thus, the role of core polyadenylation signals could be more passive than commonly believed. Our results provide new insights into the mechanisms of alternative polyadenylation and expand the catalog of related aberrations. Abbreviations APA: alternative polyadenylation; bp: basepair; MEF: mouse embryonic fibroblasts; PA: polyadenylation; PAS: polyadenylation site; Pol II: (RNA) polymerase II ; RT-PCR:reverse-transcriptase PCR; SF:splicing factor; SFPQ:splicing factor rich in proline and glutamine; SS:splice site; TRSM:Thymidine rich sequence motif; UTR:untranslated terminal region
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Affiliation(s)
- Carmen Mora Gallardo
- Department of Immunology and Oncology Centro Nacional De Biotecnología (CNB)/, CSIC Darwin 3, Campus UAM Cantoblanco, Madrid, Spain
| | - Ainhoa Sánchez de Diego
- Department of Immunology and Oncology Centro Nacional De Biotecnología (CNB)/, CSIC Darwin 3, Campus UAM Cantoblanco, Madrid, Spain
| | - Carlos Martínez-A
- Department of Immunology and Oncology Centro Nacional De Biotecnología (CNB)/, CSIC Darwin 3, Campus UAM Cantoblanco, Madrid, Spain
| | - Karel H M van Wely
- Department of Immunology and Oncology Centro Nacional De Biotecnología (CNB)/, CSIC Darwin 3, Campus UAM Cantoblanco, Madrid, Spain
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14
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Albanese KI, Waters ML. Contributions of methionine to recognition of trimethyllysine in aromatic cage of PHD domains: implications of polarizability, hydrophobicity, and charge on binding. Chem Sci 2021; 12:8900-8908. [PMID: 34257891 PMCID: PMC8246079 DOI: 10.1039/d1sc02175c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 05/27/2021] [Indexed: 11/21/2022] Open
Abstract
Recognition of trimethyllysine (Kme3) by reader proteins is an important regulator of gene expression. This recognition event is mediated by an aromatic cage made up of 2-4 aromatic residues in the reader proteins that bind Kme3 via cation-π interactions. A small subset of reader proteins contain a methionine (Met) residue in place of an aromatic sidechain in the binding pocket. The unique role of sulfur in molecular recognition has been demonstrated in a number of noncovalent interactions recently, including interactions of thiols, thioethers, and sulfoxides with aromatic rings. However, the interaction of a thioether with an ammonium ion has not previously been investigated and the role of Met in binding Kme3 has not yet been explored. Herein, we systematically vary the Met in two reader proteins, DIDO1 and TAF3, and the ligand, Kme3 or its neutral analog tert-butyl norleucine (tBuNle), to determine the role of Met in the recognition of the cationic Kme3. Our studies demonstrate that Met contributes to binding via dispersion forces, with about an equal contribution to binding Kme3 and tBuNle, indicating that electrostatic interactions do not play a role. During the course of these studies, we also discovered that DIDO1 exhibits equivalent binding to tBuNle and Kme3 through a change in the mechanism of binding.
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Affiliation(s)
- Katherine I Albanese
- Department of Chemistry, University of North Carolina at Chapel Hill CB 3290 Chapel Hill NC 27599 USA
| | - Marcey L Waters
- Department of Chemistry, University of North Carolina at Chapel Hill CB 3290 Chapel Hill NC 27599 USA
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15
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Abstract
Gene transcription by RNA polymerase II (Pol II) is the first step in the expression of the eukaryotic genome and a focal point for cellular regulation during development, differentiation, and responses to the environment. Two decades after the determination of the structure of Pol II, the mechanisms of transcription have been elucidated with studies of Pol II complexes with nucleic acids and associated proteins. Here we provide an overview of the nearly 200 available Pol II complex structures and summarize how these structures have elucidated promoter-dependent transcription initiation, promoter-proximal pausing and release of Pol II into active elongation, and the mechanisms that Pol II uses to navigate obstacles such as nucleosomes and DNA lesions. We predict that future studies will focus on how Pol II transcription is interconnected with chromatin transitions, RNA processing, and DNA repair.
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Affiliation(s)
- Sara Osman
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany;,
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany;,
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16
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Jain K, Fraser CS, Marunde MR, Parker MM, Sagum C, Burg JM, Hall N, Popova IK, Rodriguez KL, Vaidya A, Krajewski K, Keogh MC, Bedford MT, Strahl BD. Characterization of the plant homeodomain (PHD) reader family for their histone tail interactions. Epigenetics Chromatin 2020; 13:3. [PMID: 31980037 PMCID: PMC6979384 DOI: 10.1186/s13072-020-0328-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 01/13/2020] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Plant homeodomain (PHD) fingers are central "readers" of histone post-translational modifications (PTMs) with > 100 PHD finger-containing proteins encoded by the human genome. Many of the PHDs studied to date bind to unmodified or methylated states of histone H3 lysine 4 (H3K4). Additionally, many of these domains, and the proteins they are contained in, have crucial roles in the regulation of gene expression and cancer development. Despite this, the majority of PHD fingers have gone uncharacterized; thus, our understanding of how these domains contribute to chromatin biology remains incomplete. RESULTS We expressed and screened 123 of the annotated human PHD fingers for their histone binding preferences using reader domain microarrays. A subset (31) of these domains showed strong preference for the H3 N-terminal tail either unmodified or methylated at H3K4. These H3 readers were further characterized by histone peptide microarrays and/or AlphaScreen to comprehensively define their H3 preferences and PTM cross-talk. CONCLUSIONS The high-throughput approaches utilized in this study establish a compendium of binding information for the PHD reader family with regard to how they engage histone PTMs and uncover several novel reader domain-histone PTM interactions (i.e., PHRF1 and TRIM66). This study highlights the usefulness of high-throughput analyses of histone reader proteins as a means of understanding how chromatin engagement occurs biochemically.
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Affiliation(s)
- Kanishk Jain
- Department of Biochemistry and Biophysics, The University of North Carolina, Chapel Hill, NC, 27599, USA.,Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Caroline S Fraser
- Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA.,Curriculum in Genetics and Molecular Biology, The University of North Carolina, Chapel Hill, NC, 27599, USA
| | | | - Madison M Parker
- Department of Biochemistry and Biophysics, The University of North Carolina, Chapel Hill, NC, 27599, USA.,Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Cari Sagum
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | | | | | | | | | | | - Krzysztof Krajewski
- Department of Biochemistry and Biophysics, The University of North Carolina, Chapel Hill, NC, 27599, USA
| | | | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA.
| | - Brian D Strahl
- Department of Biochemistry and Biophysics, The University of North Carolina, Chapel Hill, NC, 27599, USA. .,Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA. .,Curriculum in Genetics and Molecular Biology, The University of North Carolina, Chapel Hill, NC, 27599, USA.
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17
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Yu Z, Hübner J, Herrero S, Gourain V, Fischer R. On the role of the global regulator RlcA in red-light sensing in Aspergillus nidulans. Fungal Biol 2020; 124:447-457. [PMID: 32389307 DOI: 10.1016/j.funbio.2019.12.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 12/17/2019] [Accepted: 12/21/2019] [Indexed: 02/02/2023]
Abstract
A large proportion of fungal genomes are under the control of light. Most fungi employ complex light sensing systems, consisting of red-, blue-, and in some cases green-light photoreceptors. Here we studied the light response in Aspergillus nidulans. In a genetic screen, followed by whole-genome sequencing we identified a global regulator, which appears to be involved in chromatin structure modification. We therefore named the protein RlcA (regulator of light sensing and chromatin remodeling). The protein comprises a nuclear localization signal, a PHD (plant homeodomain) finger, a TFSII (found in the central region of the transcription elongation factor S-II), and a SPOC domain (Spen paralog and ortholog C-terminal domain). In the mutant, where light-controlled genes were constitutively active, the SPOC domain is missing. RlcA localized to the nucleus and interacted with the phytochrome FphA. The PHD-finger domain probably binds to trimethylated lysine 4 of histone H3, whereas the TFSII domain binds RNA polymerase II. The SPOC domain could mediate interaction with a global repressor protein. In the mutant, repressor recruitment would be hindered, whereas in the wild type repressor release would be induced after light stimulation. Our results add another layer of complexity to light sensing in filamentous fungi.
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Affiliation(s)
- Zhenzhong Yu
- Karlsruhe Institute of Technology (KIT) - South Campus Institute for Applied Biosciences Dept. of Microbiology, Fritz-Haber-Weg 4, D-76131, Karlsruhe, Germany; Nanjing Agricultural University, Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, College of Resources and Environmental Sciences, 210095, Nanjing, China.
| | - Jennifer Hübner
- Karlsruhe Institute of Technology (KIT) - South Campus Institute for Applied Biosciences Dept. of Microbiology, Fritz-Haber-Weg 4, D-76131, Karlsruhe, Germany
| | - Satur Herrero
- Karlsruhe Institute of Technology (KIT) - South Campus Institute for Applied Biosciences Dept. of Microbiology, Fritz-Haber-Weg 4, D-76131, Karlsruhe, Germany
| | - Victor Gourain
- Institute of Toxicology and GeneticsKarlsruhe Institute of Technology Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Reinhard Fischer
- Karlsruhe Institute of Technology (KIT) - South Campus Institute for Applied Biosciences Dept. of Microbiology, Fritz-Haber-Weg 4, D-76131, Karlsruhe, Germany.
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18
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Mora Gallardo C, Sánchez de Diego A, Gutiérrez Hernández J, Talavera-Gutiérrez A, Fischer T, Martínez-A C, van Wely KHM. Dido3-dependent SFPQ recruitment maintains efficiency in mammalian alternative splicing. Nucleic Acids Res 2019; 47:5381-5394. [PMID: 30931476 PMCID: PMC6547428 DOI: 10.1093/nar/gkz235] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 03/19/2019] [Accepted: 03/22/2019] [Indexed: 12/12/2022] Open
Abstract
Alternative splicing is facilitated by accessory proteins that guide spliceosome subunits to the primary transcript. Many of these splicing factors recognize the RNA polymerase II tail, but SFPQ is a notable exception even though essential for mammalian RNA processing. This study reveals a novel role for Dido3, one of three Dido gene products, in alternative splicing. Binding of the Dido3 amino terminus to histones and to the polymerase jaw domain was previously reported, and here we show interaction between its carboxy terminus and SFPQ. We generated a mutant that eliminates Dido3 but preserves other Dido gene products, mimicking reduced Dido3 levels in myeloid neoplasms. Dido mutation suppressed SFPQ binding to RNA and increased skipping for a large group of exons. Exons bearing recognition sequences for alternative splicing factors were nonetheless included more efficiently. Reduced SFPQ recruitment may thus account for increased skipping of SFPQ-dependent exons, but could also generate a splicing factor surplus that becomes available to competing splice sites. Taken together, our data indicate that Dido3 is an adaptor that controls SFPQ utilization in RNA splicing. Distributing splicing factor recruitment over parallel pathways provides mammals with a simple mechanism to regulate exon usage while maintaining RNA splicing efficiency.
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Affiliation(s)
- Carmen Mora Gallardo
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB)/CSIC, Darwin 3, Campus UAM Cantoblanco, 28049 Madrid, Spain
| | - Ainhoa Sánchez de Diego
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB)/CSIC, Darwin 3, Campus UAM Cantoblanco, 28049 Madrid, Spain
| | - Julio Gutiérrez Hernández
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB)/CSIC, Darwin 3, Campus UAM Cantoblanco, 28049 Madrid, Spain
| | - Amaia Talavera-Gutiérrez
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB)/CSIC, Darwin 3, Campus UAM Cantoblanco, 28049 Madrid, Spain
| | - Thierry Fischer
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB)/CSIC, Darwin 3, Campus UAM Cantoblanco, 28049 Madrid, Spain
| | - Carlos Martínez-A
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB)/CSIC, Darwin 3, Campus UAM Cantoblanco, 28049 Madrid, Spain
| | - Karel H M van Wely
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB)/CSIC, Darwin 3, Campus UAM Cantoblanco, 28049 Madrid, Spain
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19
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Yu X, Martin PGP, Michaels SD. BORDER proteins protect expression of neighboring genes by promoting 3' Pol II pausing in plants. Nat Commun 2019; 10:4359. [PMID: 31554790 PMCID: PMC6761125 DOI: 10.1038/s41467-019-12328-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 08/30/2019] [Indexed: 12/18/2022] Open
Abstract
Ensuring that one gene's transcription does not inappropriately affect the expression of its neighbors is a fundamental challenge to gene regulation in a genomic context. In plants, which lack homologs of animal insulator proteins, the mechanisms that prevent transcriptional interference are not well understood. Here we show that BORDER proteins are enriched in intergenic regions and prevent interference between closely spaced genes on the same strand by promoting the 3' pausing of RNA polymerase II at the upstream gene. In the absence of BORDER proteins, 3' pausing associated with the upstream gene is reduced and shifts into the promoter region of the downstream gene. This is consistent with a model in which BORDER proteins inhibit transcriptional interference by preventing RNA polymerase from intruding into the promoters of downstream genes.
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Affiliation(s)
- Xuhong Yu
- Department of Biology, Indiana University, 915 East Third Street, Bloomington, IN, 47405, USA
| | - Pascal G P Martin
- Department of Biology, Indiana University, 915 East Third Street, Bloomington, IN, 47405, USA.,Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, 31027, Toulouse, France
| | - Scott D Michaels
- Department of Biology, Indiana University, 915 East Third Street, Bloomington, IN, 47405, USA.
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20
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Wang W, Walmacq C, Chong J, Kashlev M, Wang D. Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II. Proc Natl Acad Sci U S A 2018; 115:E2538-E2545. [PMID: 29487211 PMCID: PMC5856558 DOI: 10.1073/pnas.1722050115] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Abasic sites are among the most abundant DNA lesions and interfere with DNA replication and transcription, but the mechanism of their action on transcription remains unknown. Here we applied a combined structural and biochemical approach for a comprehensive investigation of how RNA polymerase II (Pol II) processes an abasic site, leading to slow bypass of lesion. Encounter of Pol II with an abasic site involves two consecutive slow steps: insertion of adenine opposite a noninstructive abasic site (the A-rule), followed by extension of the 3'-rAMP with the next cognate nucleotide. Further studies provided structural insights into the A-rule: ATP is slowly incorporated into RNA in the absence of template guidance. Our structure revealed that ATP is bound to the Pol II active site, whereas the abasic site is located at an intermediate state above the Bridge Helix, a conserved structural motif that is cirtical for Pol II activity. The next extension step occurs in a template-dependent manner where a cognate substrate is incorporated, despite at a much slower rate compared with nondamaged template. During the extension step, neither the cognate substrate nor the template base is located at the canonical position, providing a structural explanation as to why this step is as slow as the insertion step. Taken together, our studies provide a comprehensive understanding of Pol II stalling and bypass of the abasic site in the DNA template.
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Affiliation(s)
- Wei Wang
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Celine Walmacq
- Center for Cancer Research, National Cancer Institute, Frederick, MD 21702
| | - Jenny Chong
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Mikhail Kashlev
- Center for Cancer Research, National Cancer Institute, Frederick, MD 21702
| | - Dong Wang
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093;
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093
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21
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Appling FD, Schneider DA, Lucius AL. Multisubunit RNA Polymerase Cleavage Factors Modulate the Kinetics and Energetics of Nucleotide Incorporation: An RNA Polymerase I Case Study. Biochemistry 2017; 56:5654-5662. [PMID: 28846843 DOI: 10.1021/acs.biochem.7b00370] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
All cellular RNA polymerases are influenced by protein factors that stimulate RNA polymerase-catalyzed cleavage of the nascent RNA. Despite divergence in amino acid sequence, these so-called "cleavage factors" appear to share a common mechanism of action. Cleavage factors associate with the polymerase through a conserved structural element of the polymerase known as the secondary channel or pore. This mode of association enables the cleavage factor to reach through the secondary channel into the polymerase active site to reorient the active site divalent metal ions. This reorientation converts the polymerase active site into a nuclease active site. Interestingly, eukaryotic RNA polymerases I and III (Pols I and III, respectively) have incorporated their cleavage factors as bona fide subunits known as A12.2 and C11, respectively. Although it is clear that A12.2 and C11 dramatically stimulate the polymerase's cleavage activity, it is not known if or how these subunits affect the polymerization mechanism. In this work we have used transient-state kinetic techniques to characterize a Pol I isoform lacking A12.2. Our data clearly demonstrate that the A12.2 subunit profoundly affects the kinetics and energetics of the elementary steps of Pol I-catalyzed nucleotide incorporation. Given the high degree of conservation between polymerase-cleavage factor interactions, these data indicate that cleavage factor-modulated nucleotide incorporation mechanisms may be common to all cellular RNA polymerases.
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Affiliation(s)
- Francis D Appling
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham , Birmingham, Alabama 35294, United States
| | - David A Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham , Birmingham, Alabama 35294, United States
| | - Aaron L Lucius
- Department of Chemistry, University of Alabama at Birmingham , Birmingham, Alabama 35294, United States
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22
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Tencer AH, Gatchalian J, Klein BJ, Khan A, Zhang Y, Strahl BD, van Wely KHM, Kutateladze TG. A Unique pH-Dependent Recognition of Methylated Histone H3K4 by PPS and DIDO. Structure 2017; 25:1530-1539.e3. [PMID: 28919441 DOI: 10.1016/j.str.2017.08.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 07/26/2017] [Accepted: 08/15/2017] [Indexed: 01/07/2023]
Abstract
The protein partner of Sans-fille (PPS) and its human homolog DIDO mediate diverse chromatin activities, including the regulation of stemness genes in embryonic stem cells and splicing in Drosophila. Here, we show that the PHD fingers of PPS and DIDO recognize the histone mark H3K4me3 in a pH-dependent manner: the binding is enhanced at high pH values but is decreased at low pH. Structural analysis reveals that the pH dependency is due to the presence of a histidine residue in the K4me3-binding aromatic cage of PPS. The pH-dependent mechanism is conserved in DIDO but is lost in yeast Bye1. Acidification of cells leads to the accelerated efflux of endogenous DIDO, indicating the pH-dependent sensing of H3K4me3 in vivo. This novel mode for the recognition of H3K4me3 establishes the PHD fingers of PPS and DIDO as unique epigenetic readers and high pH sensors and suggests a role for the histidine switch during mitosis.
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Affiliation(s)
- Adam H Tencer
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Jovylyn Gatchalian
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Brianna J Klein
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Abid Khan
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Yi Zhang
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Brian D Strahl
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Karel H M van Wely
- Department of Immunology and Oncology, Centro Nacional de Biotecnología/CSIC, 28049 Madrid, Spain
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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23
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Cornett EM, Dickson BM, Rothbart SB. Analysis of Histone Antibody Specificity with Peptide Microarrays. J Vis Exp 2017. [PMID: 28809825 DOI: 10.3791/55912] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Post-translational modifications (PTMs) on histone proteins are widely studied for their roles in regulating chromatin structure and gene expression. The mass production and distribution of antibodies specific to histone PTMs has greatly facilitated research on these marks. As histone PTM antibodies are key reagents for many chromatin biochemistry applications, rigorous analysis of antibody specificity is necessary for accurate data interpretation and continued progress in the field. This protocol describes an integrated pipeline for the design, fabrication and use of peptide microarrays for profiling the specificity of histone antibodies. The design and analysis aspects of this procedure are facilitated by ArrayNinja, an open-source and interactive software package we recently developed to streamline the customization of microarray print formats. This pipeline has been used to screen a large number of commercially available and widely used histone PTM antibodies, and data generated from these experiments are freely available through an online and expanding Histone Antibody Specificity Database. Beyond histones, the general methodology described herein can be applied broadly to the analysis of PTM-specific antibodies.
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24
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Fütterer A, de Celis J, Navajas R, Almonacid L, Gutiérrez J, Talavera-Gutiérrez A, Pacios-Bras C, Bernascone I, Martin-Belmonte F, Martinéz-A C. DIDO as a Switchboard that Regulates Self-Renewal and Differentiation in Embryonic Stem Cells. Stem Cell Reports 2017; 8:1062-1075. [PMID: 28330622 PMCID: PMC5390109 DOI: 10.1016/j.stemcr.2017.02.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 02/15/2017] [Accepted: 02/16/2017] [Indexed: 12/28/2022] Open
Abstract
Transition from symmetric to asymmetric cell division requires precise coordination of differential gene expression. We show that embryonic stem cells (ESCs) mainly express DIDO3 and that their differentiation after leukemia inhibitory factor withdrawal requires DIDO1 expression. C-terminal truncation of DIDO3 (Dido3ΔCT) impedes ESC differentiation while retaining self-renewal; small hairpin RNA-Dido1 ESCs have the same phenotype. Dido3ΔCT ESC differentiation is rescued by ectopic expression of DIDO3, which binds the Dido locus via H3K4me3 and RNA POL II and induces DIDO1 expression. DIDO1, which is exported to cytoplasm, associates with, and is N-terminally phosphorylated by PKCiota. It binds the E3 ubiquitin ligase WWP2, which contributes to cell fate by OCT4 degradation, to allow expression of primitive endoderm (PE) markers. PE formation also depends on phosphorylated DIDO3 localization to centrosomes, which ensures their correct positioning for PE cell polarization. We propose that DIDO isoforms act as a switchboard that regulates genetic programs for ESC transition from pluripotency maintenance to promotion of differentiation. DIDO3 regulates DIDO1 expression Cytoplasmic DIDO1 promotes cell fate DIDO3 regulates centrosome position DIDO1 and DIDO3 are phosphorylated by PKCiota
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Affiliation(s)
- Agnes Fütterer
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, 28049 Madrid, Spain
| | - Jésus de Celis
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, 28049 Madrid, Spain
| | - Rosana Navajas
- Proteomics Unit, ProteoRed ISCIII, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, 28049 Madrid, Spain
| | - Luis Almonacid
- Genomics Unit, Q-PCR Facility, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, 28049 Madrid, Spain
| | - Julio Gutiérrez
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, 28049 Madrid, Spain
| | - Amaia Talavera-Gutiérrez
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, 28049 Madrid, Spain
| | - Cristina Pacios-Bras
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, 28049 Madrid, Spain
| | - Ilenia Bernascone
- Department of Development and Differentiation, Centro de Biología Molecular Severo Ochoa, CSIC-Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Fernando Martin-Belmonte
- Department of Development and Differentiation, Centro de Biología Molecular Severo Ochoa, CSIC-Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Carlos Martinéz-A
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, 28049 Madrid, Spain.
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25
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Harlen KM, Churchman LS. Subgenic Pol II interactomes identify region-specific transcription elongation regulators. Mol Syst Biol 2017; 13:900. [PMID: 28043953 PMCID: PMC5293154 DOI: 10.15252/msb.20167279] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Transcription, RNA processing, and chromatin‐related factors all interact with RNA polymerase II (Pol II) to ensure proper timing and coordination of transcription and co‐transcriptional processes. Many transcription elongation regulators must function simultaneously to coordinate these processes, yet few strategies exist to explore the complement of factors regulating specific stages of transcription. To this end, we developed a strategy to purify Pol II elongation complexes from subgenic regions of a single gene, namely the 5′ and 3′ regions, using sequences in the nascent RNA. Applying this strategy to Saccharomyces cerevisiae, we determined the specific set of factors that interact with Pol II at precise stages during transcription. We identify many known region‐specific factors as well as determine unappreciated associations of regulatory factors during early and late stages of transcription. These data reveal a role for the transcription termination factor, Rai1, in regulating the early stages of transcription genome‐wide and support the role of Bye1 as a negative regulator of early elongation. We also demonstrate a role for the ubiquitin ligase, Bre1, in regulating Pol II dynamics during the latter stages of transcription. These data and our approach to analyze subgenic transcription elongation complexes will shed new light on the myriad factors that regulate the different stages of transcription and coordinate co‐transcriptional processes.
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Affiliation(s)
- Kevin M Harlen
- Department of Genetics, Harvard Medical School, Boston, MA, USA
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26
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Plaschka C, Hantsche M, Dienemann C, Burzinski C, Plitzko J, Cramer P. Transcription initiation complex structures elucidate DNA opening. Nature 2016; 533:353-8. [DOI: 10.1038/nature17990] [Citation(s) in RCA: 180] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 04/08/2016] [Indexed: 12/19/2022]
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27
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Hwang CS, Xu L, Wang W, Ulrich S, Zhang L, Chong J, Shin JH, Huang X, Kool ET, McKenna CE, Wang D. Functional interplay between NTP leaving group and base pair recognition during RNA polymerase II nucleotide incorporation revealed by methylene substitution. Nucleic Acids Res 2016; 44:3820-8. [PMID: 27060150 PMCID: PMC4857003 DOI: 10.1093/nar/gkw220] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 03/18/2016] [Accepted: 03/21/2016] [Indexed: 02/07/2023] Open
Abstract
RNA polymerase II (pol II) utilizes a complex interaction network to select and incorporate correct nucleoside triphosphate (NTP) substrates with high efficiency and fidelity. Our previous 'synthetic nucleic acid substitution' strategy has been successfully applied in dissecting the function of nucleic acid moieties in pol II transcription. However, how the triphosphate moiety of substrate influences the rate of P-O bond cleavage and formation during nucleotide incorporation is still unclear. Here, by employing β,γ-bridging atom-'substituted' NTPs, we elucidate how the methylene substitution in the pyrophosphate leaving group affects cognate and non-cognate nucleotide incorporation. Intriguingly, the effect of the β,γ-methylene substitution on the non-cognate UTP/dT scaffold (∼3-fold decrease in kpol) is significantly different from that of the cognate ATP/dT scaffold (∼130-fold decrease in kpol). Removal of the wobble hydrogen bonds in U:dT recovers a strong response to methylene substitution of UTP. Our kinetic and modeling studies are consistent with a unique altered transition state for bond formation and cleavage for UTP/dT incorporation compared with ATP/dT incorporation. Collectively, our data reveals the functional interplay between NTP triphosphate moiety and base pair hydrogen bonding recognition during nucleotide incorporation.
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Affiliation(s)
- Candy S Hwang
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089-0744, USA
| | - Liang Xu
- Department of Cellular and Molecular Medicine, School of Medicine; Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California, San Diego, La Jolla, CA 92093-0625, USA
| | - Wei Wang
- Department of Cellular and Molecular Medicine, School of Medicine; Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California, San Diego, La Jolla, CA 92093-0625, USA
| | - Sébastien Ulrich
- Department of Chemistry, Stanford University, Stanford, CA 94305-5017, USA Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université Montpellier, ENSCM, Ecole Nationale Supérieure de Chimie de Montpellier, 8 Rue de l'Ecole Normale, 34296 Montpellier cedex 5, France
| | - Lu Zhang
- Department of Chemistry, Division of Biomedical Engineering, Center of Systems Biology and Human Health, School of Science and Institute for Advance Study, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Jenny Chong
- Department of Cellular and Molecular Medicine, School of Medicine; Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California, San Diego, La Jolla, CA 92093-0625, USA
| | - Ji Hyun Shin
- Department of Cellular and Molecular Medicine, School of Medicine; Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California, San Diego, La Jolla, CA 92093-0625, USA
| | - Xuhui Huang
- Department of Chemistry, Division of Biomedical Engineering, Center of Systems Biology and Human Health, School of Science and Institute for Advance Study, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305-5017, USA
| | - Charles E McKenna
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089-0744, USA
| | - Dong Wang
- Department of Cellular and Molecular Medicine, School of Medicine; Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California, San Diego, La Jolla, CA 92093-0625, USA
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28
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Liu B, Zuo Y, Steitz TA. Structures of E. coli σS-transcription initiation complexes provide new insights into polymerase mechanism. Proc Natl Acad Sci U S A 2016; 113:4051-6. [PMID: 27035955 PMCID: PMC4839411 DOI: 10.1073/pnas.1520555113] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In bacteria, multiple σ factors compete to associate with the RNA polymerase (RNAP) core enzyme to form a holoenzyme that is required for promoter recognition. During transcription initiation RNAP remains associated with the upstream promoter DNA via sequence-specific interactions between the σ factor and the promoter DNA while moving downstream for RNA synthesis. As RNA polymerase repetitively adds nucleotides to the 3'-end of the RNA, a pyrophosphate ion is generated after each nucleotide incorporation. It is currently unknown how the release of pyrophosphate affects transcription. Here we report the crystal structures of E coli transcription initiation complexes (TICs) containing the stress-responsive σ(S) factor, a de novo synthesized RNA oligonucleotide, and a complete transcription bubble (σ(S)-TIC) at about 3.9-Å resolution. The structures show the 3D topology of the σ(S) factor and how it recognizes the promoter DNA, including likely specific interactions with the template-strand residues of the -10 element. In addition, σ(S)-TIC structures display a highly stressed pretranslocated initiation complex that traps a pyrophosphate at the active site that remains closed. The position of the pyrophosphate and the unusual phosphodiester linkage between the two terminal RNA residues suggest an unfinished nucleotide-addition reaction that is likely at equilibrium between nucleotide addition and pyrophosphorolysis. Although these σ(S)-TIC crystals are enzymatically active, they are slow in nucleotide addition, as suggested by an NTP soaking experiment. Pyrophosphate release completes the nucleotide addition reaction and is associated with extensive conformational changes around the secondary channel but causes neither active site opening nor transcript translocation.
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Affiliation(s)
- Bin Liu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - Yuhong Zuo
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520;
| | - Thomas A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520; Department of Chemistry, Yale University, New Haven, CT 06520
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29
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Wozniak GG, Strahl BD. Hitting the ‘mark’: Interpreting lysine methylation in the context of active transcription. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1353-61. [DOI: 10.1016/j.bbagrm.2014.03.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 03/01/2014] [Accepted: 03/03/2014] [Indexed: 12/31/2022]
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30
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Pinskaya M, Ghavi-Helm Y, Mariotte-Labarre S, Morillon A, Soutourina J, Werner M. PHD and TFIIS-Like domains of the Bye1 transcription factor determine its multivalent genomic distribution. PLoS One 2014; 9:e102464. [PMID: 25029256 PMCID: PMC4100922 DOI: 10.1371/journal.pone.0102464] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 06/19/2014] [Indexed: 11/18/2022] Open
Abstract
The BYpass of Ess1 (Bye1) protein is a putative S. cerevisiae transcription factor homologous to the human cancer-associated PHF3/DIDO family of proteins. Bye1 contains a Plant Homeodomain (PHD) and a TFIIS-like domain. The Bye1 PHD finger interacts with tri-methylated lysine 4 of histone H3 (H3K4me3) while the TFIIS-like domain binds to RNA polymerase (Pol) II. Here, we investigated the contribution of these structural features to Bye1 recruitment to chromatin as well as its function in transcriptional regulation. Genome-wide analysis of Bye1 distribution revealed at least two distinct modes of association with actively transcribed genes: within the core of Pol II- and Pol III-transcribed genes concomitant with the presence of the TFIIS transcription factor and, additionally, with promoters of a subset of Pol II-transcribed genes. Specific loss of H3K4me3 abolishes Bye1 association to gene promoters, but doesn't affect its binding within gene bodies. Genetic interactions suggested an essential role of Bye1 in cell fitness under stress conditions compensating the absence of TFIIS. Furthermore, BYE1 deletion resulted in the attenuation of GAL genes expression upon galactose-mediated induction indicating its positive role in transcription regulation. Together, these findings point to a bimodal role of Bye1 in regulation of Pol II transcription. It is recruited via its PHD domain to H3K4 tri-methylated promoters at early steps of transcription. Once Pol II is engaged into elongation, Bye1 binds directly to the transcriptional machinery, modulating its progression along the gene.
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Affiliation(s)
- Marina Pinskaya
- iBiTec-S CEA, FRE3377, Gif-sur-Yvette, France
- CNRS, FRE3377, Gif-sur-Yvette, France
- Université Paris-Sud, FRE3377, Gif-sur-Yvette, France
- ncRNA, epigenetic and genome fluidity, Institut Curie, Centre de Recherche, CNRS UMR3244, Université Pierre et Marie Curie, Paris, France
- * E-mail: (MW); (MP)
| | - Yad Ghavi-Helm
- iBiTec-S CEA, FRE3377, Gif-sur-Yvette, France
- CNRS, FRE3377, Gif-sur-Yvette, France
- Université Paris-Sud, FRE3377, Gif-sur-Yvette, France
| | - Sylvie Mariotte-Labarre
- iBiTec-S CEA, FRE3377, Gif-sur-Yvette, France
- CNRS, FRE3377, Gif-sur-Yvette, France
- Université Paris-Sud, FRE3377, Gif-sur-Yvette, France
| | - Antonin Morillon
- ncRNA, epigenetic and genome fluidity, Institut Curie, Centre de Recherche, CNRS UMR3244, Université Pierre et Marie Curie, Paris, France
| | - Julie Soutourina
- iBiTec-S CEA, FRE3377, Gif-sur-Yvette, France
- CNRS, FRE3377, Gif-sur-Yvette, France
- Université Paris-Sud, FRE3377, Gif-sur-Yvette, France
| | - Michel Werner
- iBiTec-S CEA, FRE3377, Gif-sur-Yvette, France
- CNRS, FRE3377, Gif-sur-Yvette, France
- Université Paris-Sud, FRE3377, Gif-sur-Yvette, France
- * E-mail: (MW); (MP)
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31
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Abstract
The Ess1 prolyl isomerase from Saccharomyces cerevisiae and its human ortholog, Pin1, play critical roles in transcription by regulating RNA polymerase II. In human cells, Pin1 also regulates a variety of signaling proteins, and Pin1 misexpression is linked to several human diseases. To gain insight into Ess1/Pin1 function, we carried out a synthetic genetic array screen to identify novel targets of Ess1 in yeast. We identified potential targets of Ess1 in transcription, stress, and cell-cycle pathways. We focused on the cell-cycle regulators Swi6 and Whi5, both of which show highly regulated nucleocytoplasmic shuttling during the cell cycle. Surprisingly, Ess1 did not control their transcription but instead was necessary for their nuclear localization. Ess1 associated with Swi6 and Whi5 in vivo and bound directly to peptides corresponding to their nuclear localization sequences in vitro. Binding by Ess1 was significant only if the Swi6 and Whi5 peptides were phosphorylated at Ser-Pro motifs, the target sites of cyclin-dependent kinases. On the basis of these results, we propose a model in which Ess1 induces a conformational switch (cis-trans isomerization) at phospho-Ser-Pro sites within the nuclear targeting sequences of Swi6 and Whi5. This switch would promote nuclear entry and/or retention during late M and G1 phases and might work by stimulating dephosphorylation at these sites by the Cdc14 phosphatase. This is the first study to identify targets of Ess1 in yeast other than RNA polymerase II.
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32
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Rothbart SB, Strahl BD. Interpreting the language of histone and DNA modifications. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:627-43. [PMID: 24631868 DOI: 10.1016/j.bbagrm.2014.03.001] [Citation(s) in RCA: 499] [Impact Index Per Article: 45.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 02/14/2014] [Accepted: 03/04/2014] [Indexed: 01/10/2023]
Abstract
A major mechanism regulating the accessibility and function of eukaryotic genomes are the covalent modifications to DNA and histone proteins that dependably package our genetic information inside the nucleus of every cell. Formally postulated over a decade ago, it is becoming increasingly clear that post-translational modifications (PTMs) on histones act singly and in combination to form a language or 'code' that is read by specialized proteins to facilitate downstream functions in chromatin. Underappreciated at the time was the level of complexity harbored both within histone PTMs and their combinations, as well as within the proteins that read and interpret the language. In addition to histone PTMs, newly-identified DNA modifications that can recruit specific effector proteins have raised further awareness that histone PTMs operate within a broader language of epigenetic modifications to orchestrate the dynamic functions associated with chromatin. Here, we highlight key recent advances in our understanding of the epigenetic language encompassing histone and DNA modifications and foreshadow challenges that lie ahead as we continue our quest to decipher the fundamental mechanisms of chromatin regulation. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.
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Affiliation(s)
- Scott B Rothbart
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Brian D Strahl
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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33
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The Ess1 prolyl isomerase: traffic cop of the RNA polymerase II transcription cycle. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:316-33. [PMID: 24530645 DOI: 10.1016/j.bbagrm.2014.02.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2014] [Revised: 02/01/2014] [Accepted: 02/03/2014] [Indexed: 11/23/2022]
Abstract
Ess1 is a prolyl isomerase that regulates the structure and function of eukaryotic RNA polymerase II. Ess1 works by catalyzing the cis/trans conversion of pSer5-Pro6 bonds, and to a lesser extent pSer2-Pro3 bonds, within the carboxy-terminal domain (CTD) of Rpb1, the largest subunit of RNA pol II. Ess1 is conserved in organisms ranging from yeast to humans. In budding yeast, Ess1 is essential for growth and is required for efficient transcription initiation and termination, RNA processing, and suppression of cryptic transcription. In mammals, Ess1 (called Pin1) functions in a variety of pathways, including transcription, but it is not essential. Recent work has shown that Ess1 coordinates the binding and release of CTD-binding proteins that function as co-factors in the RNA pol II complex. In this way, Ess1 plays an integral role in writing (and reading) the so-called CTD code to promote production of mature RNA pol II transcripts including non-coding RNAs and mRNAs.
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